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PhylogeneticEM 1.7.0

• Bug fixes:
  • Fix documentation notes on CRAN checks.
• New functions and features:
  • Function node_optimal_values for optimal values computation at each nodes.
  • Trait names are now inherited by the params_process objects.

PhylogeneticEM 1.6.0

• Deprecation fix:
  • Update code to comply with Matrix 1.4-2 new coding standards.
• API change:
  • Function compute_stationary_variance now always return a dpoMatrix, using Matrix::nearPD if needed. The change only impacts computations with full variance and selection strength matrices, which are never used in a typical PhyloEM analysis, but could impact direct calls to the function or simulations under complex scenarios.
• Bug Fix:
  • In plot.equivalent_shifts make sure the colors of the regimes are consistent for all equivalent solutions.

PhylogeneticEM 1.5.0

• Bug fix:
  • merge_rotations now accepts datasets with entire species missing, and throws an error when the missing data pattern is not compatible with a rotation.
• Warnings:
  • The function now throws a warning when two traits are very highly correlated.
• CI:
  • Replace Travis with Github Actions.
  • Build doc automatically with GHA.

PhylogeneticEM 1.4.0

• New option:
  • Add an option “show_axis_traits” to control the trait axis in a plot.
• New Feature
  • Function simul_process can now handle an “OU/BM” process (i.e. an OU with some eigen values equal to zero).
• Bug fix:
  • Documented arguments not in usage in documentation object equivalent_shifts.
  • Check with “R_CHECK_FORCE_SUGGESTS=FALSE” now runs.

PhylogeneticEM 1.3.0

• Bug fix:
  • Bug fix in plot function for univariate result.
  • Tree does not need to be ultrametric for a BM
  • Change tol to tol_EM in estimateEM for actual binding
  • Bug fixes in plot function for displaying traits.
• New Option:
  • Add option “name_trait” to plot function for ancestral state reconstruction.
• API Change
  • For a univariate trait, the BM re-scaling is now applied by default.
• Deprecation Fix:
  • Update ape, and replace is.binary.tree by is.binary.
  • Remove dependency to Rphylopars (no longer on CRAN).

PhylogeneticEM 1.2.1

• CRAN maintenance
  • Added references in Description
  • Reduce checking and vignette building time

PhylogeneticEM 1.2.0

• Added Options:
  • option_is.ultrametric to control the ape::is.ultrametric check.
• Deprecation Fix:
  • Go back to updated version of gglasso (faster than grplasso). This should not change the results of PhylogeneticEM.
• Added functions:
  • Functions find_rotation and merge_rotations to deal with datasets that are equal up to a rotation.
  • Functions get_criterion and plot_criterion to get and plot the criterion used for model selection easily.
• New feature:
  • Function PhyloEM can now allow for negative values of alpha, to fit an EB model.
• Bug fix:
  • In function plot, fixed bug that led to the wrong parameters being selected when doing ancestral trait reconstruction.

PhylogeneticEM 1.1.0

• Deprecation Fix:
  • Remove dependency from gglasso (replaced with grplasso). This should not change the results of PhylogeneticEM.
• Bug Fixes:
  • Issue an error message when the tree has some zero-length branches.
• Minor Changes:
  • Added options to plot.equivalent_shifts.

PhylogeneticEM 1.0.1

• Minor Changes:
  • Impose a maximum value for alpha in find_grid_alpha to respect machine max double.
• New Features
  • added argument label_font to plot function to control the label font.
  • added argument axis_las to plot function to control the axis las.
• Bug fixes:
  • Plotting missing values correctly in plot.PhyloEM.
  • Bug fixes in plotting PhyloEM object when p = 1.
  • When p=1 and nbr_alpha is not missing, do not switch to estimated mode for alpha.
• Technical:
  • registration of c++ code to comply with R 3.4 new standards.

PhylogeneticEM 1.0.0

Initial Release.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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